Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Astro"
graph_weight
## [1] "0.5"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   32.00   35.00   37.00   36.30   37.25   40.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 32 32 32 33 33 33 34 34 35 35 35 36 36 36 36 36 37 37 37 37 37 37 37 37 37
## [26] 37 37 37 37 37 38 38 38 38 38 38 38 40 40 40

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1643   357
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1622   357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:       BTBD11       ABTB3
##  2:    LINC01006    RNF32-DT
##  3:    LINC01185      REL-DT
##  4:   ZRANB2-AS2   ZRANB2-DT
##  5:    LINC00271     AHI1-DT
##  6:     RFX3-AS1     RFX3-DT
##  7:    COX10-AS1    COX10-DT
##  8:   SUCLG2-AS1   SUCLG2-DT
##  9:      C5orf17   LINC02899
## 10:     OSMR-AS1     OSMR-DT
## 11:  C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2   TENM2-AS1
## 13:    LINC00637 PPP1R13B-DT
## 14:         MPP6    MPHOSPH6
## 15:      C7orf61      SPACDR
## 16:      C3orf35       APRG1
## 17:       HRAT92    PDGFA-DT
## 18:    LINC00884  ATP13A3-DT
## 19:    LINC01137  ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21:      MAFG-DT       MILIP
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
## 3:        ASB4      ASB4        ASB4
## 4:       USH1C     USH1C       USH1C
## 5:    ARHGAP44  ARHGAP44    ARHGAP44
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene              6900 0.118699020              90.14412
## 2:            gene               161 0.002485395              99.77003
##    total_counts
## 1:         8310
## 2:          174
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
##   0.00857  90.44551  99.20296  90.72478  99.93429 100.00000 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   60.04   81.87   72.81   92.88   97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:         A2M       A2M         A2M ENSG00000175899               FALSE
## 2:   A2ML1-AS1 A2ML1-AS1   A2ML1-AS1 ENSG00000256661               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              5826   0.1207987
## 2:    NCBITaxon:9606            gene             11030   0.2138297
##    pct_dropout_by_counts total_counts selected
## 1:              91.67821         8457        1
## 2:              84.24488        14970        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "PRKAR2B"     "NRXN3"       "ELAVL2"      "MMP16"       "CADPS"      
##  [6] "CCSER1"      "SYT1"        "MAP2"        "RBFOX1"      "PDE1A"      
## [11] "RIMS3"       "DPP6"        "LRRC4B"      "SNTG1"       "CACNA1B"    
## [16] "RBFOX3"      "GRM5"        "NLGN1"       "FRMPD4"      "DLGAP1"     
## [21] "ARPP21"      "CNTNAP2"     "RIMS2"       "CSMD1"       "OPCML"      
## [26] "KCNH7"       "RALYL"       "SYN3"        "KCNIP4"      "ELAVL3"     
## [31] "RYR2"        "MEG3"        "RP1-30E17.2" "IQCJ-SCHIP1"

## [1] 2
##  [1] "SLC26A3"              "STEAP1B"              "TFCP2L1"             
##  [4] "ZSWIM4"               "NKD1"                 "CCDC3"               
##  [7] "ESYT3"                "SYTL3"                "SEMA3E"              
## [10] "SLC26A5"              "FRMD3"                "RTN4RL1"             
## [13] "PLK5"                 "NWD1"                 "AC023469.1"          
## [16] "AC003991.3"           "AC104088.1"           "AC002127.4"          
## [19] "RP11-154D17.1"        "EPCAM-DT"             "RP11-384F7.1"        
## [22] "ALDH1L1-AS2"          "RP11-17A1.3"          "RP11-26J3.1"         
## [25] "RP11-20D14.3"         "RP11-507B12.2"        "CASC17"              
## [28] "CEACAM16-AS1"         "MIR23AHG"             "CTD-2189E23.1"       
## [31] "RMRP_ENSG00000269900" "SPANXA2-OT1"          "RP11-154H23.4"       
## [34] "RP11-596C23.6"        "RP4-799O8.1"          "RP11-465L10.14"      
## [37] "RP3-466I7.2"

## [1] 3
##  [1] "PSD"           "SEZ6L"         "SLC2A9"        "ST6GALNAC5"   
##  [5] "KIRREL3"       "MAP3K7CL"      "SYNPR"         "NDST3"        
##  [9] "GRIK2"         "METTL2B"       "NEGR1"         "CALN1"        
## [13] "SGCZ"          "SLIT1"         "ERC2"          "DLGAP2"       
## [17] "FBXO16"        "RP11-170M17.1" "AC011288.2"    "LINC01503"    
## [21] "MSC-AS1"       "RP11-20I20.2"  "RP11-586K2.1"  "RP4-809F18.1" 
## [25] "PWRN1"         "GEMIN7-AS1"    "SYNPO2L-AS1"   "RP11-640F22.1"
## [29] "RP11-320L2.1"  "CLIP2"         "TGIF2"         "UNC13C"       
## [33] "SLC6A9"        "AJAP1"         "ODAD4"         "KRTAP5-AS1"

## [1] 4
##  [1] "WARS1"                   "HDAC9"                  
##  [3] "CDON"                    "TMEM38A"                
##  [5] "ITPKC"                   "CATSPERG"               
##  [7] "CDKL1"                   "PADI2"                  
##  [9] "KLHL29"                  "RAP1GAP2"               
## [11] "TMTC1"                   "KIAA0513"               
## [13] "SLC44A5"                 "CBLN2"                  
## [15] "BOC"                     "SEC24D"                 
## [17] "ZNF385D"                 "ST3GAL2"                
## [19] "FBXO27"                  "EDIL3"                  
## [21] "GPR176"                  "ATOH8"                  
## [23] "GPR137C"                 "SPATA13_ENSG00000182957"
## [25] "ZBTB7C"                  "CACNA1E"                
## [27] "MEF2B"                   "RP11-191L9.4"           
## [29] "RP11-513I15.6"           "NRSN2-AS1"              
## [31] "LINC00685"               "RP5-864K19.4"           
## [33] "RP11-147G16.1"           "CTC-340A15.2"           
## [35] "RP11-79E3.2"             "DGCR5_ENSG00000273032"  
## [37] "CASTOR2"

## [1] 5
##  [1] "LRRC7"         "PON3"          "PLAGL1"        "MAEL"         
##  [5] "SLC9B1"        "SCN11A"        "FSTL5"         "CATSPERE"     
##  [9] "COL5A2"        "AC012593.1"    "ZRANB2-AS2"    "MIR181A1HG"   
## [13] "LINC01036"     "RAP2C-AS1"     "UFL1-AS1"      "PPP1R9A-AS1"  
## [17] "RP11-4B14.3"   "PTPRG-AS1"     "RP11-167H9.4"  "H2AZ1-DT"     
## [21] "RP11-461O7.1"  "LINC00504"     "LINC02144"     "CTB-161M19.4" 
## [25] "RP11-380P13.1" "C8orf37-AS1"   "AB015752.3"    "LINC02740"    
## [29] "RP11-260G13.1" "RP11-525K10.3" "ADGRL1-AS1"    "RP11-103J8.1" 
## [33] "RP11-964E11.3" "RP4-681L3.3"   "RP4-660H19.2"  "RP1-84D21.2"  
## [37] "RP11-120J1.2"  "C1orf87"

## [1] 6
##  [1] "SP140"          "SEL1L2"         "ANKRD7"         "PAPPA2"        
##  [5] "RGS22"          "SAXO1"          "MEGF11"         "PKD1L1"        
##  [9] "SPATA17"        "OTOGL"          "ODAD2"          "GPR39"         
## [13] "ENO4"           "SCOC-AS1"       "LEKR1"          "LINC01876"     
## [17] "RP11-162D16.2"  "LINC01277"      "AC079807.4"     "LINC00271"     
## [21] "RP11-154D6.1"   "LINC01358"      "RP11-446H18.5"  "LINC01340"     
## [25] "LINC00534"      "CTB-178M22.2"   "RP11-727A23.10" "LINC02745"     
## [29] "RP11-352M15.1"  "LINC02320"      "SPESP1"         "RP11-524F11.2" 
## [33] "LINC00907"      "LINC00506"      "RP11-444C24.1"  "RP11-335E8.3"  
## [37] "AC064875.2"     "TSBP1-AS1"

## [1] 7
##  [1] "ASB4"     "HSD11B1"  "PLK2"     "ZCCHC18"  "SP140L"   "KCNG1"   
##  [7] "SYNE2"    "CDH3"     "NGEF"     "ZFY"      "RASGRP2"  "ARHGAP15"
## [13] "ANGPT2"   "PCDH11Y"  "NAMPT"    "ARID3A"   "TNNT2"    "KIAA1217"
## [19] "HS3ST2"   "AIF1L"    "C1QL1"    "SLC6A6"   "ANXA1"    "SRRM4"   
## [25] "RIT2"     "FBXO32"   "CATIP"    "SPATA2L"  "ITGA5"    "REPS2"   
## [31] "VAT1L"    "NXNL1"    "PCP4"     "POTEG"    "AFAP1"    "STARD10"

## [1] 8
##  [1] "MT3"     "EPM2A"   "ACAT2"   "GFRA1"   "GRIA4"   "DLC1"    "ANO5"   
##  [8] "PTPRN"   "PIR"     "DOK5"    "GLIS3"   "B4GALT2" "MACF1"   "NCAN"   
## [15] "NAV1"    "CCNH"    "SOX5"    "HAVCR2"  "TMOD1"   "SSH2"    "TIAM2"  
## [22] "CNNM2"   "ABR"     "SPTBN4"  "OXR1"    "FAT3"    "SLC20A2" "CRADD"  
## [29] "PFKFB3"  "FRMD5"   "MYO1D"   "SAMD12"  "KCNQ5"   "WWOX"    "S100A10"
## [36] "EML6"

## [1] 9
##  [1] "TESC"         "P3H2"         "CHRNE"        "WASF1"        "IL1R1"       
##  [6] "HELB"         "TICAM1"       "GALNT8"       "PTPRE"        "TTC9"        
## [11] "IRAK2"        "TTLL7"        "AK7"          "ITPRIP"       "ADAM12"      
## [16] "PLCL2"        "LRGUK"        "CFAP161"      "CFAP251"      "ORAI2"       
## [21] "TMCO4"        "SHISA5"       "NFIL3"        "TMC1"         "DEPP1"       
## [26] "COL24A1"      "PRIMA1"       "TSHZ2"        "MAFF"         "OVCH1"       
## [31] "RASGEF1A"     "NHSL2"        "TCEA3"        "MIR34AHG"     "SATB1-AS1"   
## [36] "RP11-403A3.3"

## [1] 10
##  [1] "CEMIP"         "COL4A2"        "UNC5D"         "SGCD"         
##  [5] "MACROD2"       "RNLS"          "RP11-111A21.1" "RP11-692P14.1"
##  [9] "PLXNA2"        "SYT17"         "COBL"          "LGI1"         
## [13] "PRR12"         "HIP1"          "ZSWIM6"        "MAPK4"        
## [17] "SDK1"          "FAM13C"        "THRB"          "RHPN1"        
## [21] "AHCYL2"        "RFTN2"         "FAM107A"       "FAXDC2"       
## [25] "FAM222B"       "SYT12"         "IQCK"          "FIGN"         
## [29] "SLC25A18"      "LHFPL6"        "FLRT2"         "DMWD"         
## [33] "ARHGEF26-AS1"  "STX18-AS1"     "AGBL1"

## [1] 11
##  [1] "EFCAB11"       "C11orf65"      "DNAH12"        "LINC01006"    
##  [5] "RHCE"          "HMGN5"         "CRPPA"         "AC105760.2"   
##  [9] "LINC01185"     "AC008269.2"    "LINC01239"     "RP1-230L10.1" 
## [13] "NECTIN3-AS1"   "RP11-550I24.2" "RP11-436F23.1" "LINC02196"    
## [17] "LINC02615"     "CTC-347C20.1"  "LINC02326"     "RP11-16B13.1" 
## [21] "IDH2-DT"       "CRTC3-AS1"     "AC004158.3"    "PLS3-AS1"     
## [25] "LINC02664"     "CTC-428H11.2"  "CTD-2313D3.2"  "RP11-788A4.3" 
## [29] "RP11-168F16.1" "LMNTD1"        "TVP23A"        "GSG1L"        
## [33] "TOGARAM2"      "AP000318.2"    "RP11-348F1.3"  "RP11-190P13.2"
## [37] "RP11-148E17.1" "RP11-210M15.2"

## [1] 12
##  [1] "RNF175"        "RETREG1"       "GPC6"          "GRM7"         
##  [5] "SYT7"          "ATP9A"         "FRY"           "RASL12"       
##  [9] "ATRNL1"        "ABCC3"         "MAN1C1"        "GFPT2"        
## [13] "SCN2A"         "SCN1A"         "SLC4A10"       "ZNF385B"      
## [17] "CDH18"         "CNTN5"         "SLC24A2"       "MYO1E"        
## [21] "NFASC"         "PGM2L1"        "KIF5C"         "TPST1"        
## [25] "SLCO3A1"       "SLC8A1"        "PDE2A"         "SHTN1"        
## [29] "NHS"           "PTPRT"         "LINC00632"     "TNFRSF25"     
## [33] "AC067956.1"    "SHISA9"        "PTCHD4"        "LINC01411"    
## [37] "LINC02506"     "RP11-624C23.1"

## [1] 13
##  [1] "IL7"           "MT1G"          "APOE"          "CCDC59"       
##  [5] "PDE5A"         "SYCP2L"        "GLRX"          "PLD5"         
##  [9] "PROS1"         "EYS"           "HES4"          "F5"           
## [13] "LUCAT1"        "RP11-624D11.2" "LINC02389"     "GAS7"         
## [17] "RHOBTB1"       "KNOP1"         "TSHZ3"         "HIVEP3"       
## [21] "DIAPH2"        "PXDNL"         "ART3"          "SLC5A11"      
## [25] "PDPN"          "ABCA1"         "LINGO1"        "DPYD"         
## [29] "TMEM229B"      "MMP17"         "LINC01320"     "LINC01322"

## [1] 14
##  [1] "CPED1"         "SPATA6L"       "F3"            "SLC14A1"      
##  [5] "SLC44A3"       "SLC22A3"       "SLC43A2"       "FTH1"         
##  [9] "ERICH3"        "CCBE1"         "WNT7B"         "MAMDC2-AS1"   
## [13] "MALRD1"        "SOX1-OT"       "CHL1-AS2"      "PPP1R26-AS1"  
## [17] "XIST"          "OBI1-AS1"      "LINC01934"     "RP11-390F4.6" 
## [21] "SUCLG2-AS1"    "BAALC-AS1"     "LINC01182"     "LINC00923"    
## [25] "LINC00499"     "GS1-57L11.1"   "RP11-156K13.1" "RMST"         
## [29] "RP11-798K3.2"  "AC007193.6"    "RP11-496B10.6" "RP11-382N13.7"
## [33] "RP11-563M4.2"

## [1] 15
##  [1] "XK"            "BCAS1"         "PCSK1N"        "SRPX2"        
##  [5] "CALY"          "CHST9"         "CHODL"         "FREM1"        
##  [9] "VWA3A"         "NPSR1-AS1"     "TSBP1"         "MT1H"         
## [13] "RNF212B"       "RP4-660H19.1"  "RP11-735G4.1"  "RP11-106M7.1" 
## [17] "RP11-141A19.1" "DPP10-AS3"     "DIRC3"         "LINC01524"    
## [21] "DPP10-AS1"     "RP11-475C16.2" "RP11-624M8.1"  "LINC02877"    
## [25] "PRKAR2B-AS1"   "LINC02355"     "RP11-114J13.1" "RP11-711G10.1"
## [29] "LINC02715"     "MAP1LC3B2"     "LINC01579"     "DIO2-AS1"     
## [33] "RP11-80I3.1"   "RP11-290O12.2" "SLC7A14-AS1"   "RP11-725F23.1"
## [37] "RP11-875G18.1" "RP5-892C22.1"

## [1] 16
##  [1] "PUDP"           "ADRA1B"         "LRRC3B"         "EPS15-AS1"     
##  [5] "RP11-134O21.1"  "RP11-242P2.1"   "CH17-174L20.1"  "CTD-2126E3.6"  
##  [9] "RP11-624A4.2"   "WFDC1"          "XYLT1"          "CPEB3"         
## [13] "RIPOR2"         "DMGDH"          "LGR6"           "KCNJ16"        
## [17] "PID1"           "GNA14"          "MRAS"           "PTCHD1"        
## [21] "CHST11"         "LRRC8C"         "HPSE2"          "FZD8"          
## [25] "CTD-2527I21.15" "LDLRAD3"        "NME9"           "TMEM184B"      
## [29] "PLIN5"          "LINC00511"      "HPN-AS1"        "PTCHD1-AS"     
## [33] "AC016745.3"     "LINC02208"      "RP11-237N2.1"   "RP11-183J19.1" 
## [37] "RP11-404C6.6"

## [1] 17
##  [1] "USH1C"       "DNAH9"       "SLC39A14"    "CAP2"        "PHACTR2"    
##  [6] "UBE3D"       "ELL2"        "MGAT3"       "CA3"         "LRRN2"      
## [11] "GPR156"      "C9orf153"    "RP1-223B1.1" "TRMT9B"      "CD99"       
## [16] "KLF6"        "AEBP1"       "SUFU"        "ZFP36"       "QRICH2"     
## [21] "ZBTB46"      "RFTN1"       "GMPR"        "EGF"         "GABPB2"     
## [26] "ZNF208"      "WNK2"        "LDLRAD4"     "IFFO2"       "SYNM"       
## [31] "RGS6"        "ZNF594-DT"

## [1] 18
##  [1] "IDI1"          "DPH6"          "FADS2"         "C2CD6"        
##  [5] "ALDH1A1"       "PAH"           "CYP7B1"        "CASC2"        
##  [9] "COL25A1"       "CC2D2B"        "DCHS2"         "FIRRE"        
## [13] "AC004540.5"    "COL28A1"       "POT1-AS1"      "LYPLAL1-DT"   
## [17] "LINC01344"     "AC007682.1"    "RFX3-AS1"      "COX10-AS1"    
## [21] "LINC01376"     "AC079305.11"   "RNF217-AS1"    "RP11-268P4.5" 
## [25] "RP11-284M14.1" "RP11-679C8.2"  "RP11-582J16.4" "RP11-404I7.2" 
## [29] "RP11-673E1.1"  "ZFHX4-AS1"     "RP11-157I4.4"  "RP11-541P9.3" 
## [33] "MPPED2-AS1"    "RP11-511B23.2" "LINC02328"     "CTC-498M16.4" 
## [37] "RP3-383B8.1"   "CTD-2297M2.1"

## [1] 19
##  [1] "BAIAP3"         "USH2A"          "FAP"            "KLF2"          
##  [5] "RHBDL3"         "FAM151B"        "GAL3ST2"        "DRC1"          
##  [9] "LRRC2"          "NPNT"           "NOTUM"          "PAX8-AS1"      
## [13] "LAMA2"          "C3orf35"        "LINC00862"      "CFI"           
## [17] "RP11-174G6.1"   "AC003090.1"     "RP11-69I8.3"    "RP1-35C21.2"   
## [21] "CYP1B1-AS1"     "LINC01137"      "IQCM"           "L3MBTL2-AS1"   
## [25] "RP11-279O9.4"   "LINC02315"      "LINC02356"      "RP11-499F3.2"  
## [29] "RP1-158P9.2"    "RP11-876N24.2"  "RP11-60A24.3"   "KLF2-DT"       
## [33] "CH507-528H12.1" "RP11-114N1.1"   "RP11-301F14.1"  "CTD-2201E18.6" 
## [37] "RP11-4D11.1"

## [1] 20
##  [1] "RRAGD"         "CALCRL"        "SIDT1"         "WSCD2"        
##  [5] "SLC8A3"        "PLCB4"         "GDAP1L1"       "SLC24A4"      
##  [9] "ADAMTS9"       "GUCY1A1"       "GFRA2"         "DELEC1"       
## [13] "CYP4F12"       "CYP4F3"        "INSYN2B"       "RP11-344B5.2" 
## [17] "LINC01630"     "LINC01768"     "LINC00326"     "DIRC3-AS1"    
## [21] "AC007563.5"    "RP11-154H17.1" "LINC02814"     "SOCS2-AS1"    
## [25] "RP11-1252I4.2" "RP11-124B13.1" "RP11-708B6.2"  "LINC02327"    
## [29] "FRMD6-AS2"     "MAPT-AS1"      "RP11-354K4.2"  "RP11-323P17.2"
## [33] "LINC00836"     "CTC-490G23.6"  "RP11-492O8.3"  "RP11-259G3.1" 
## [37] "RP11-154D6.3"  "RP11-609L3.3"  "RP1-20N4.2"    "RP11-423B13.1"

## [1] 21
##  [1] "GABRE"    "FAXC"     "HESX1"    "PBX3"     "GTF2IRD1" "PLEKHA5" 
##  [7] "ATP2B4"   "PDE4A"    "CERS4"    "MYO9B"    "PALM"     "ARHGEF18"
## [13] "PLIN3"    "ZMIZ1"    "CCND3"    "NFIC"     "ITPKB"    "CTDSPL"  
## [19] "ABCB9"    "AKAP6"    "JAZF1"    "CLSTN2"   "ADCY9"    "PKNOX2"  
## [25] "DHRSX"    "PTPN9"    "NPAS2"    "KCND3"    "PACS1"    "CMTM4"   
## [31] "OSBP2"    "RILPL1"   "PARVA"    "LIME1"    "NEAT1"    "CUX1"    
## [37] "FBXO17"

## [1] 22
##  [1] "UPP2"           "EPHA6"          "CABLES1"        "RERG"          
##  [5] "C4orf19"        "MN1"            "RNF150"         "SLC24A3"       
##  [9] "HDHD5-AS1"      "GRM3"           "AC074391.1"     "AP001628.6"    
## [13] "SOX21-AS1"      "AP000282.2"     "RP11-498J9.2"   "RPL34-DT"      
## [17] "RP11-142A5.1"   "LINC00886"      "RP11-11N9.4"    "LINC02234"     
## [21] "CTC-329D1.2"    "HS3ST5"         "RP11-130F10.1"  "F11-AS1"       
## [25] "LINC01301"      "RP1-84O15.2"    "RP11-317N12.1"  "RP11-431M3.1"  
## [29] "RP11-526N18.1"  "CTD-2349P21.11" "LINC01727"      "RP11-281A20.2" 
## [33] "RP11-437L7.2"   "RP11-1289C17.1" "RP11-346I3.7"   "EBF4"          
## [37] "OLFM2"

## [1] 23
##  [1] "GBE1"     "SCLT1"    "CMSS1"    "CNTN1"    "SAMD4A"   "DGKG"    
##  [7] "KIF3C"    "PCSK5"    "GAB1"     "TPD52L1"  "WLS"      "FOXO3"   
## [13] "PDZRN3"   "PALLD"    "CEP350"   "TNS3"     "BCAS3"    "FAM171A1"
## [19] "ZEB1"     "FOXO1"    "CACNB2"   "ZNF608"   "PCDH7"    "ZFPM2"   
## [25] "GNG7"     "NCKAP5"   "RGMA"     "CADM1"    "IRS2"     "TPCN1"   
## [31] "HRH1"     "ZNF785"   "PLCG2"    "DNM3"     "TOX"

## [1] 24
##  [1] "NID1"           "MOGAT1"         "MTERF1"         "TMEM241"       
##  [5] "MFSD4B"         "SUGCT"          "DLEU1"          "DIO2"          
##  [9] "HEPN1"          "RP1-292B18.4"   "RP11-131L23.1"  "MRPS9-AS2"     
## [13] "TMLHE-AS1"      "LINC01266"      "PLCG1-AS1"      "HDAC2-AS2"     
## [17] "RP4-613B23.1"   "GNA14-AS1"      "GNG12-AS1"      "LINC00513"     
## [21] "LINC01937"      "GS1-433O24.1"   "PKN2-AS1"       "ZBTB20-AS5"    
## [25] "RORA-AS1"       "MEF2C-AS2"      "LIX1-AS1"       "RP11-804N13.1" 
## [29] "AP000462.2"     "RP11-315E17.1"  "RP11-39M21.1"   "TSIX"          
## [33] "RP11-470M1.2"   "RP11-57G22.3"   "RP11-793H13.14" "RP11-341N18.1" 
## [37] "RP11-399K19.1"

## [1] 25
##  [1] "ANOS1"    "MAOB"     "SEMA3A"   "TRPM3"    "MROH8"    "SCG3"    
##  [7] "DHRS7B"   "SLC1A2"   "LAMA4"    "TACR1"    "DNAH7"    "ENOX1"   
## [13] "GTDC1"    "TMEM108"  "BEND6"    "C10orf90" "WIF1"     "IGFBP7"  
## [19] "TSPAN5"   "RGS7"     "IMMP2L"   "ROR1"     "KLHL32"   "VKORC1L1"
## [25] "ATP1A2"   "ARHGAP31" "TBC1D1"   "SEMA3C"   "PHACTR3"  "ZBTB16"  
## [31] "C1orf21"  "RIN2"     "SHROOM3"  "SEMA3D"   "ENOX2"    "SRGAP1"  
## [37] "EFCAB2"

## [1] 26
##  [1] "FILIP1L"       "GLIPR1L1"      "SEPTIN1"       "AC002463.3"   
##  [5] "RP11-547I7.1"  "ST7-AS2"       "AC105461.1"    "AC017101.10"  
##  [9] "CCDC192"       "RP11-417B4.2"  "RP11-46O21.2"  "GRM3-AS1"     
## [13] "PCDH9-AS4"     "RP11-666F17.1" "RP11-109I13.2" "STARD13-AS"   
## [17] "LINC02652"     "LINC00960"     "RP11-768G7.3"  "GK-AS1"       
## [21] "RP11-115N4.1"  "RP11-274H2.2"  "ANK2-AS1"      "MAPK10-AS1"   
## [25] "RP11-39E3.3"   "RP11-351A11.1" "CTD-3239E11.2" "RP11-452H21.1"
## [29] "RP11-463D19.1" "RP11-513G19.1" "A2ML1-AS1"     "RP11-887P2.5" 
## [33] "PRKCA-AS1"     "RP11-138H11.1" "LINC01374"     "RP11-576O3.1" 
## [37] "RP11-394G3.3"  "RP11-555K12.4"

## [1] 27
##  [1] "ATP11A"        "PDE8B"         "KCTD1"         "ARRDC4"       
##  [5] "SPOCK1"        "LMOD1"         "ADAP2"         "SHISA6"       
##  [9] "CTA-292E10.6"  "LMCD1-AS1"     "OSMR-AS1"      "MALAT1"       
## [13] "RP11-175O15.1" "ADGRL1"        "TRHDE"         "RFX2"         
## [17] "DAAM1"         "CDH20"         "UNC5B"         "RFX4"         
## [21] "ADGRB3"        "ENSA"          "DENND2A"       "FLCN"         
## [25] "NAV2"          "MOB3A"         "CADM2"         "SPACA6"       
## [29] "MAML2"         "KIF9-AS1"      "AC004951.6"    "LINC00342"    
## [33] "HMGA1P4"       "RP3-414A15.10" "RP11-35G9.5"   "ATP6V0D1-DT"  
## [37] "RP11-514P8.10"

## [1] 28
##  [1] "PPEF1"    "EPB41L4B" "GALNT16"  "FRK"      "EYA4"     "SIPA1L2" 
##  [7] "APOC1"    "EPSTI1"   "AXDND1"   "EPHX4"    "SYN1"     "DCN"     
## [13] "RRP12"    "RIMBP2"   "ABCA7"    "ATP2B3"   "PPP1R15A" "CASS4"   
## [19] "KAT8"     "ISYNA1"   "EPHB6"    "CLNK"     "PPFIBP1"  "CHD5"    
## [25] "DUSP1"    "CDKN1A"   "MICAL1"   "BIN1"     "SLC43A1"  "DOC2A"   
## [31] "CACNB3"   "DUSP8"    "HAUS7"

## [1] 29
##  [1] "TACC2"         "SNHG31"        "COL23A1"       "RARB"         
##  [5] "SESN1"         "GRK3"          "CAB39L"        "MPP6"         
##  [9] "LIN7A"         "PACRG"         "ARSB"          "SEM1"         
## [13] "IQCA1"         "ARHGAP29"      "GLTP"          "CLVS2"        
## [17] "C2CD2"         "NRG2"          "ADORA1"        "CKB"          
## [21] "PDE3A"         "CALCB"         "ANO6"          "PPP1R42"      
## [25] "CCDC30"        "KBTBD12"       "NKAIN2"        "ZNF358"       
## [29] "LYRM4"         "LINC00598"     "WARS2-AS1"     "DLEU2"        
## [33] "LINC01135"     "RP11-507B12.1" "RP11-379B18.8" "RP11-358F13.1"
## [37] "RP11-166M16.1"

## [1] 30
##  [1] "CD38"          "HHAT"          "ARHGAP28"      "ANKRD24"      
##  [5] "ZFR2"          "KIAA1549L"     "PEX5L"         "DNAH6"        
##  [9] "TFAP2E"        "TRIM22"        "PEBP4"         "PLXNC1"       
## [13] "DNAAF1"        "KIF6"          "JAM3"          "VWA3B"        
## [17] "GRIK1"         "ZBTB44-DT"     "CIITA"         "PCED1B"       
## [21] "PRELID2"       "SLC4A5"        "MAML3"         "RP1-167A14.2" 
## [25] "TARID"         "AF131217.1"    "LINC01725"     "LINC00407"    
## [29] "DRAIC"         "RP4-785G19.5"  "LINC00958"     "RP11-396B14.2"
## [33] "RP1-41C23.1"   "RP11-239A17.1" "RP11-274G22.1" "RP11-125D12.3"
## [37] "RP11-373E16.6" "RP11-255O19.2" "ARHGEF3"       "LINC01094"

## [1] 31
##  [1] "BNC2"          "MCUB"          "VCAN"          "ARHGAP6"      
##  [5] "KITLG"         "ST6GALNAC2"    "ST6GAL1"       "CCL2"         
##  [9] "JHY"           "PRRX1"         "SOHLH2"        "LRAT"         
## [13] "ST18"          "CCDC175"       "SAMD3"         "SLITRK5"      
## [17] "FBN1"          "TEKT1"         "HTR1E"         "RCAN2"        
## [21] "CAVIN1"        "PLCXD3"        "CHST6"         "CCK"          
## [25] "SAMD11"        "PLPP4"         "AP001347.6"    "RP1-187B23.1" 
## [29] "RP11-146I2.1"  "AL163953.3"    "LINC01088"     "CTB-35F21.1"  
## [33] "LINC00609"     "RP1-79C4.4"    "RP11-403A3.2"  "RP5-1015P16.1"
## [37] "RP11-6L16.1"

## [1] 32
##  [1] "AHRR"          "POLR2I"        "CA1"           "LRTM1"        
##  [5] "AGBL3"         "ABI3BP"        "BTG2"          "LINC01931"    
##  [9] "SHOC1"         "CLMP"          "PAPPA"         "CARNMT1-AS1"  
## [13] "ANKUB1"        "Z83001.1"      "ASTN2-AS1"     "RP1-232L24.3" 
## [17] "AC009501.4"    "AC037445.1"    "RP5-1101C3.1"  "CTD-2015H6.3" 
## [21] "RP11-223C24.1" "RP11-348J24.1" "RP11-517I3.1"  "ZFPM2-AS1"    
## [25] "RP11-649G15.2" "BBOX1-AS1"     "CTD-2537O9.1"  "RP11-1H15.2"  
## [29] "RP11-144F15.1" "RP11-370I10.2" "RP11-184D12.1" "RP11-58G13.1" 
## [33] "CTC-513N18.6"  "CH17-140K24.2" "BCL6-AS1"      "RP11-592G13.2"
## [37] "NUP210L"

## [1] 33
##  [1] "TENT5A"        "UNC79"         "PKIB"          "ST6GAL2"      
##  [5] "HHIP"          "P2RY14"        "RFLNA"         "PNMA3"        
##  [9] "NAP1L3"        "FSIP2"         "CLDN4"         "RP11-306O13.1"
## [13] "LCNL1"         "LINC02649"     "AC072062.3"    "PCDH9-AS2"    
## [17] "GPC5-AS2"      "LINC02250"     "AC008067.2"    "RP13-143G15.4"
## [21] "RP11-657O9.1"  "LRP4-AS1"      "C1QTNF7-AS1"   "LINC01950"    
## [25] "RP11-116O11.1" "AP000487.6"    "RP11-20E24.1"  "PRANCR"       
## [29] "RP11-72M17.1"  "HIF1A-AS3"     "LINC01572"     "PSMD7-DT"     
## [33] "CTD-2282P23.2" "RP11-221G19.1" "RP11-69G16.2"  "RP11-314E10.1"

## [1] 34
##  [1] "MAMLD1"        "BID"           "GAB2"          "MYO16"        
##  [5] "PPM1H"         "DPYSL3"        "EEPD1"         "ABCC4"        
##  [9] "FAM117B"       "TMEM132B"      "STOX2"         "LIPE-AS1"     
## [13] "APTR"          "TENM3"         "AQP1"          "MRPL33"       
## [17] "RP11-410D17.2" "MGAM"          "RASAL2"        "HSD17B14"     
## [21] "MAST3"         "BNIP3L"        "UBE2R2"        "SH3PXD2A"     
## [25] "CCDC146"       "ARHGAP26"      "MAGI1"         "TIAM1"        
## [29] "DHRS3"         "PLEKHA7"       "GNG4"          "SLC35E3"      
## [33] "ABAT"          "ANKS1B"        "MAPT"

## [1] 35
##  [1] "TENM1"     "MRC2"      "CCDC85A"   "NTN1"      "RIPK2"     "RASD1"    
##  [7] "NT5DC3"    "RGS4"      "ID1"       "TMEM160"   "TRIM5"     "CHI3L1"   
## [13] "BEX1"      "TESPA1"    "RNF165"    "LYPD6B"    "ARHGAP27"  "CCDC141"  
## [19] "FABP5"     "PRTG"      "SCG5"      "VWCE"      "GINS3"     "STAC3"    
## [25] "IL1RAPL2"  "SVIL"      "KCNMB2"    "BAALC-AS2" "LRRC24"    "FGF17"    
## [31] "SPSB1"     "YOD1"      "FAM110C"

## [1] 36
##  [1] "RP11-436D23.1"         "COL5A3"                "LAMB4"                
##  [4] "LRMDA"                 "FREM2"                 "KCNE4"                
##  [7] "TDRD9"                 "RANBP3L"               "CSDC2"                
## [10] "TRDN"                  "ZNF98"                 "LINC01208"            
## [13] "ARL17B"                "SPRY4-AS1"             "PDYN-AS1"             
## [16] "KCNMB2-AS1"            "MEIKIN"                "ETV5"                 
## [19] "KCNK15-AS1"            "TMEM161B-AS1"          "RP11-446J8.1"         
## [22] "RP11-346L1.2"          "MTRNR2L1"              "RP11-328J6.1"         
## [25] "RPPH1_ENSG00000259001" "TAPT1-AS1"             "MAFG-DT"              
## [28] "RP11-838N2.5"          "MTRNR2L12"             "RP11-711K1.8"         
## [31] "CH507-513H4.1"         "LINC02246"             "RP1-166D18.1"         
## [34] "RP11-398J12.1"

## [1] 37
##  [1] "LIX1"             "LINC00637"        "TLE2"             "PDZD4"           
##  [5] "P2RX7"            "SEC14L5"          "SPAG1"            "AGFG2"           
##  [9] "USP9Y"            "MOB3B"            "PATJ"             "DGKB"            
## [13] "KCNH5"            "DOCK11"           "CNKSR2"           "PARP8"           
## [17] "DEPTOR"           "ADCY8"            "ZNF653"           "ADCY1"           
## [21] "CFAP47"           "NLGN4Y"           "ARMC3"            "SLC38A11"        
## [25] "TTTY14"           "UTY"              "CFAP54"           "DISP3"           
## [29] "XXbac-BPG55C20.7" "TTTY10"           "LINC00278"        "LINC00884"       
## [33] "CTD-2643I7.5"     "MIR4300HG"        "CTD-2054N24.2"    "RP11-93B21.2"    
## [37] "RP11-125C10.1"

## [1] 38
##  [1] "SNCAIP"        "BICC1"         "MT2A"          "KIAA1328"     
##  [5] "STPG2"         "MT1E"          "DPP10"         "ADD3-AS1"     
##  [9] "AC026188.1"    "LNC-LBCS"      "CCDC26"        "LINC02884"    
## [13] "RP1-45C12.1"   "MMADHC-DT"     "RP11-120D5.1"  "RP11-195C7.1" 
## [17] "SOX2-OT"       "MAILR"         "RP11-266O8.1"  "RP11-739G5.1" 
## [21] "RP11-157E16.1" "RP11-561I11.4" "RP11-378A12.1" "RP11-589M4.5" 
## [25] "RP11-574F11.4" "RNF19A"        "CTNNA2"        "ST8SIA1"      
## [29] "HIF3A"         "ARHGEF4"       "KCNN3"         "NCAM2"        
## [33] "ZNF704"        "PHYHD1"        "APOLD1"        "ZFP36L1"      
## [37] "RP11-799O21.2"

## [1] 39
##  [1] "PRKCQ"         "SLC16A6"       "WNT5B"         "HS3ST3B1"     
##  [5] "GPNMB"         "FHDC1"         "IFI44L"        "FHAD1"        
##  [9] "NTNG1"         "C4orf45"       "SNX31"         "RAB39A"       
## [13] "RFX8"          "SULT1A2"       "AC007277.3"    "SNAP25-AS1"   
## [17] "KIF5C-AS1"     "AC009264.1"    "NPIPB2"        "CDKN2B-AS1"   
## [21] "LEFTY1"        "C5orf17"       "RP11-745L13.2" "MTRNR2L8"     
## [25] "DISC1FP1"      "RP11-397A16.1" "APP-DT"        "RP11-413N10.3"
## [29] "RP11-364P22.4" "CTD-2040G12.2" "AC006296.4"    "RP11-520F22.1"

## [1] 40
##  [1] "CCDC80"        "SLC26A8"       "LRRC9"         "WDR64"        
##  [5] "CD200R1"       "IPO9-AS1"      "RP11-132E11.2" "AC092684.1"   
##  [9] "LINC01877"     "SEMA6A-AS1"    "NEUROG2-AS1"   "VCAN-AS1"     
## [13] "STPG2-AS1"     "CENATAC-DT"    "RP11-116N8.1"  "RP11-104E19.1"
## [17] "PTCSC3"        "CRIM1-DT"      "RP11-793A3.2"  "LINC00842"    
## [21] "RP5-847G17.1"  "CTD-2172F7.1"  "SLCO1A2"       "KLHL4"        
## [25] "DNAH11"        "BEST3"         "HNMT"          "ANGPT1"       
## [29] "COX7A1"        "C2"            "METTL7B"       "AC092155.4"   
## [33] "RP1-111D6.3"   "RP5-1198O20.4" "RP11-469A15.2" "RP11-90C4.1"  
## [37] "LINC02251"     "RP11-259K15.2" "RP11-627D16.1" "RP11-542F9.2"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_1"
##  [1] "PRKAR2B"     "NRXN3"       "ELAVL2"      "MMP16"       "CADPS"      
##  [6] "CCSER1"      "SYT1"        "MAP2"        "RBFOX1"      "PDE1A"      
## [11] "RIMS3"       "DPP6"        "LRRC4B"      "SNTG1"       "CACNA1B"    
## [16] "RBFOX3"      "GRM5"        "NLGN1"       "FRMPD4"      "DLGAP1"     
## [21] "ARPP21"      "CNTNAP2"     "RIMS2"       "CSMD1"       "OPCML"      
## [26] "KCNH7"       "RALYL"       "SYN3"        "KCNIP4"      "ELAVL3"     
## [31] "RYR2"        "MEG3"        "RP1-30E17.2" "IQCJ-SCHIP1"
## $reactome
##                                     category over_represented_pvalue
## 596                          neuronal system            5.219000e-07
## 725 protein protein interactions at synapses            1.386388e-05
## 595                neurexins and neuroligins            5.354203e-05
##     under_represented_pvalue numDEInCat numInCat          FDR
## 596                1.0000000         10       72 0.0005860937
## 725                0.9999994          6       25 0.0077845699
## 595                0.9999977          5       18 0.0200425653
## 
## $go_bp
##                                       category over_represented_pvalue
## 2093                neurotransmitter secretion            5.076878e-06
## 3767 regulation of synaptic vesicle exocytosis            1.013222e-05
## 4266               synaptic vesicle exocytosis            1.585970e-05
## 2094                neurotransmitter transport            2.795121e-05
## 4455     vesicle mediated transport in synapse            4.030425e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 2093                0.9999998          6       22 0.02274683
## 3767                0.9999999          4        6 0.02274683
## 4266                0.9999994          5       16 0.02373668
## 2094                0.9999983          6       29 0.03137523
## 4455                0.9999974          6       29 0.03619322
## 
## [1] "set_14"
##  [1] "CPED1"         "SPATA6L"       "F3"            "SLC14A1"      
##  [5] "SLC44A3"       "SLC22A3"       "SLC43A2"       "FTH1"         
##  [9] "ERICH3"        "CCBE1"         "WNT7B"         "MAMDC2-AS1"   
## [13] "MALRD1"        "SOX1-OT"       "CHL1-AS2"      "PPP1R26-AS1"  
## [17] "XIST"          "OBI1-AS1"      "LINC01934"     "RP11-390F4.6" 
## [21] "SUCLG2-AS1"    "BAALC-AS1"     "LINC01182"     "LINC00923"    
## [25] "LINC00499"     "GS1-57L11.1"   "RP11-156K13.1" "RMST"         
## [29] "RP11-798K3.2"  "AC007193.6"    "RP11-496B10.6" "RP11-382N13.7"
## [33] "RP11-563M4.2" 
## $reactome
##                                                                      category
## 1086 transport of bile salts and organic acids metal ions and amine compounds
## 965                                      slc mediated transmembrane transport
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1086            2.525065e-05                0.9999998          3        9
## 965             6.625814e-05                0.9999986          4       32
##             FDR
## 1086 0.02835648
## 965  0.03720395
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8954950 478.3   16112782 860.6         NA 15573326 831.8
## Vcells 16664148 127.2   31261907 238.6      65536 31261907 238.6
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0